The incident allegedly happened at Bedford South School on Thursday, May 16, during an after school program called Excel.
Jennifer Procunier told CBC News her seven-year-old son was involved in the alleged incident.
"I think we're all in shock, to be honest," she said.
Procunier said about 10 children were involved and she has spoken to several other concerned parents.
She said it's possible the children were being punished for rambunctious behaviour. Her son told her they were lined up against the wall and their mouths were taped shut.
"This is abuse," Procunier said. "You don't do that."
School board reaction questioned
Procunier said she's upset she didn't find out about the alleged incident until hours later, when her son made an offhand comment about getting in trouble during the after-school program.
"He said, 'I tried to take the tape off my mouth and as I did that I got in trouble and was told that if I took it off, I was going to get it put back on,'" she said.
Procunier said she didn't think he actually had tape on his face, and she didn't question what he meant until she spoke to another parent who said her child was taped.
"As this mother is telling me this, I almost fell through the floor. And I'm looking at our son and I can see, at this point, the marks on his face," she said.
Procunier is upset there was no notice from the school about the alleged incident.
"If we would not have approached the school board ourselves — as parents who are in the know — we would not know our son was involved."
She said her son is physically fine, but she's worried how it may affect him emotionally in the future.
Doug Hadley, a spokesman for the Halifax Regional School Board, said the board finds it unacceptable to tape children's mouths in any circumstances.
He said the assistant instructor is now on paid leave while the board and Halifax Regional Police investigate.
The allegations sparked a sharp response from Nova Scotia Education Minister Ramona Jennex.
"As the minister of education, a former teacher and a grandparent, I am very upset about this alleged incident," she said in a statement. "Our schools need to be safe havens for children in this province."
Bedford South School includes students from Grade 1 to Grade 9.